Biology subjects

Kamimura, Y.

Publications and source records attributed to Kamimura, Y..

12 recordsLinked to original sources

bioRxiv2024

Group composition and its ontogenetic changes in marine pelagic fishes

Group living is a widespread phenomenon among animals and an important trait in fishes. Understanding group composition and its dynamics is fundamental for elucidating ecological and evolutionary processes in natural populations of gregarious animal species, including fishes, but our knowledge of group composition in marine fishes is limited. Here, we examined group composition and its ontogenetic change in two marine fishes, Japanese sardine (Sardinops melanostictus) and chub mackerel (Scomber japonicus). We found that, at the juvenile stage, groups were composed of individuals with similar body length, age, and growth history. At the sub-adult stage, although body length within a group remained similar, the within-group similarity in age and growth history decreased, approaching the level expected when groups were randomly composed. Therefore, during the early life history, individuals form groups with those spawned at approximately the same time and place (i.e., those from the same batch). As they develop, however, individuals of various origins intermingle and selectively form groups with others exhibiting similar phenotypes. We further found that environmental and geographical factors were also related to the body size and age of individuals distributed. This indicates that Japanese sardine and chub mackerel exhibit phenotype-specific and growth-stage-specific habitat use, which also contributes to the formation and maintenance of structured groups. Our findings provide valuable information on group composition, its ontogenetic change, and its underlying mechanisms in marine fishes, for which the information is limited. These insights may help to clarify ecological and evolutionary processes such as population dynamics, density-dependent phenomena, and the evolution of grouping behaviour in small pelagic fishes.

ecology↗

bioRxiv2023

Dose-dependent effects of histone methyltransferase NSD2 on site-specific double-strand break repair

Histone modifications are catalyzed and recognized by specific proteins to regulate dynamic DNA metabolism processes. NSD2 is a histone H3 lysine 36 (H3K36)-specific methyltransferase that associates both with various transcription regulators and DNA repair factors. Specifically, it has been implicated in the repair of DNA double-strand breaks (DSBs); however, the role of NSD2 during DSB repair remains enigmatic. Here, we show that NSD2 does not accumulate at DSB sites and that the localization of NSD2 at chromatin is maintained even after DSB formation. Using three different DSB repair reporter systems, which contained the endonuclease site in the active thymidine kinase gene (TK) locus, we demonstrated separate dose-dependent effects of NSD2 on HR, canonical-NHEJ (c-NHEJ), and non-canonical-NHEJ (non-c-NHEJ). Endogenous NSD2 has a role in repressing non-c-NHEJ, without affecting DSB repair efficiency by HR or total NHEJ. Furthermore, overexpression of NSD2 promotes c-NHEJ repair suppressing HR repair. Therefore, we propose that NSD2 has functions in chromatin integrity at the active regions during DSB repair.

cell biology↗

bioRxiv2023

A dynamic partitioning mechanism polarizes membrane protein distribution

The plasma membrane is widely regarded as the hub of the signal transduction network activities that drives numerous physiological responses, including cell polarity and migration. Yet, the symmetry breaking process in the membrane, that leads to dynamic compartmentalization of different proteins, remains poorly understood. Using multimodal live-cell imaging, here we first show that multiple endogenous and synthetic lipid-anchored proteins, despite maintaining stable tight association with the inner leaflet of the plasma membrane, were unexpectedly depleted from the membrane domains where the signaling network was spontaneously activated such as in the new protrusions as well as within the propagating ventral waves. Although their asymmetric patterns resembled those of standard peripheral "back" proteins such as PTEN, unlike the latter, these lipidated proteins did not dissociate from the membrane upon global receptor activation. Our experiments not only discounted the possibility of recurrent reversible translocation from membrane to cytosol as it occurs for weakly bound peripheral membrane proteins, but also ruled out the necessity of directed vesicular trafficking and cytoskeletal supramolecular structure-based restrictions in driving these dynamic symmetry breaking events. Selective photoconversion-based protein tracking assays suggested that these asymmetric patterns instead originate from the inherent ability of these membrane proteins to "dynamically partition" into distinct domains within the plane of the membrane. Consistently, single-molecule measurements showed that these lipid-anchored molecules have substantially dissimilar diffusion profiles in different regions of the membrane. When these profiles were incorporated into an excitable network-based stochastic reaction-diffusion model of the system, simulations revealed that our proposed "dynamic partitioning" mechanism is sufficient to give rise to familiar asymmetric propagating wave patterns. Moreover, we demonstrated that normally uniform integral and lipid-anchored membrane proteins in Dictyostelium and mammalian neutrophil cells can be induced to partition spatiotemporally to form polarized patterns, by optogenetically recruiting membrane domain-specific peptides to these proteins. Together, our results indicate "dynamic partitioning" as a new mechanism of plasma membrane organization, that can account for large-scale compartmentalization of a wide array of lipid-anchored and integral membrane proteins in different physiological processes.

cell biology↗

bioRxiv2022

Highly structured habitats mitigate size-and growth-selective mortality of post-settlement juvenile fish

The role of vegetated habitats such as seagrass and macroalgal beds as nurseries is essential for the survival of larval and juvenile fish, although quantitative evaluation of the contribution of these habitats to nursery function is limited. Moreover, growth-survival relationships of larvae and juveniles associated with vegetated habitats have rarely been examined. To quantitatively and qualitatively evaluate the processes affecting juvenile survival in vegetated habitats, we investigated whether there is a correlation between the degree of selection for bigger and faster-growing fish and mortality rates for three cohorts by birth date of post-settlement black rockfish (Sebastes cheni) in a macroalgal bed. We also analyzed relationships between growth rate and experienced temperature by age class to examine the effects of temperature on growth. The latest cohort, which grew under lower vegetation coverage due to a seasonal increase in water temperature, showed higher mortality with evidence of strong selection for bigger and faster-growing fish. The growth-temperature relationships showed that positive effects of temperature on growth weakened after settlement. Therefore, we suggest that macroalgal coverage has a critical role controlling the growth-mortality relationship of post-settlement S. cheni. Furthermore, the negative effects of high temperature on juvenile survival through loss of vegetation may be greater than the positive effects on juvenile growth. These findings will contribute to the management of fisheries resources by increasing the understanding of relationships between survival mechanisms in fish early life stages and vegetation phenology of their habitat under the increasing effects of global warming.

ecology↗

bioRxiv2022

Density-dependent attributes of schooling in small pelagic fishes

Many small pelagic fishes obligately form schools; some of these schools attain a remarkable size. Although the school is a fundamental and important ecological unit and is the site of biological interactions such as competition and predation, information on schooling processes in the field remains scarce. Here, we examined the quantitative relationships between population density and school size, the number of schools, and other school characteristics (i.e., packing density, volume, and cross-sectional area) in three species of small pelagic fishes: Japanese anchovy Engraulis japonicus, Japanese sardine Sardinops melanostictus, and chub mackerel Scomber japonicus. We found that school size increased almost linearly with population density, whereas the number of schools and other characteristics increased non-linearly with population density, whereby the rate of increase slowed radically as population density increased. These results indicate that, at low population densities, an increase in density causes an increase in both school size and the number of schools, whereas at higher population densities, an increase in density triggers the formation of larger schools rather than more schools. Furthermore, we found that the shapes of the relationships of all school characteristics with population density differed among species. Our results indicate that the schooling behaviour of small pelagic fishes is density-dependent, and responses to changes in density are species-specific. Our results provide insight into how biological interactions such as intra- and inter-specific competition and predator-prey interactions mediate the density-dependent processes that underlie the population dynamics and community structure of small pelagic fishes in marine ecosystems.

zoology↗

bioRxiv2022

Trichomes on female reproductive tract: rapid diversification and underlying gene regulatory network in Drosophila suzukii and its related species

BackgroundThe ovipositors of some insects are external female genitalia, which have their primary function to deliver eggs. Drosophila suzukii and its sibling species D. subpulchrella are known to have acquired highly sclerotized and enlarged ovipositors upon their shifts in oviposition sites from rotting to ripening fruits. Inside the ovipositor plates, there are scale-like polarized protrusions termed "oviprovector scales" that are likely to aid the mechanical movement of the eggs. The size and spatial distribution of the scales need to be rearranged following the divergence of the ovipositors. In this study, we examined the features of the oviprovector scales in D. suzukii and its closely related species. We also investigated whether the scales are single-cell protrusions comprised of F-actin under the same conserved gene regulatory network as the well-characterized trichomes on the larval cuticular surface. ResultsThe oviprovector scales of D. suzukii and D. subpulchrella were distinct in size and spatial arrangement compared to those of a closely related species D. biarmipes and D. melanogaster. The comparisons of the size of the scales suggested that the apical cell area of the oviprovector has expanded upon the elongation of the ovipositor plates in these species. Our transcriptome analysis revealed that 43 out of the 46 genes known to be involved in the trichome gene regulatory network are expressed in the developing female genitalia of D. suzukii and D. subpulchrella. An antibody staining depicted the presence of Shavenbaby (Svb) in the inner cavity of the developing ovipositors of D. melanogaster at 44-48 h after puparium formation (APF). Also, shavenoid (sha) was expressed in the corresponding patterns in the developing ovipositors and showed differential expression levels between D. suzukii and D. subpulchrella at 48 h APF. ConclusionsThe oviprovector scales have divergent size and spatial arrangements among species. Therefore, these scales may represent a rapidly diversifying morphological trait of the female reproductive tract reflecting ecological contexts. Furthermore, our results showed that the gene regulatory network underlying trichome formation is adopted to develop the rapidly evolving trichomes on the oviprovectors of these flies.

developmental biology↗

bioRxiv2021

Stronger density-dependent growth of Japanese sardine with lower food availability: Comparison of growth and zooplankton biomass between a historical and current stock-increase period in the western North Pacific

Density dependence is a fundamental concept for fish population dynamics. Although density-dependent growth and maturity among older juveniles and adults is important for regulating fish population size and for fisheries management, the mechanism of density dependence for marine fishes remains unclear. Here, we examined changes in Japanese sardine growth with increasing abundance beginning in the 2010s and how the current pattern of density-dependent growth differs from that of a previous stock-increase period from the 1970s to early 1980s. During the current period of increasing abundance, mean standard length has already dropped to the lowest level yet observed and growth has declined more sharply with increased abundance than in the 1970s and 1980s. Mesozooplankton biomass in July in the summer feeding grounds was also lower during the current period. Therefore, our results suggest that summer food availability in the western North Pacific controls the strength of density-dependent growth. A lower carrying capacity for Japanese sardine could account for the stronger density dependence of growth observed in the 2010s; this indicates that future Japanese sardine abundance might not increase as much as in the 1980s unless food availability improves.

ecology↗

bioRxiv2021

Intra- and inter-specific density dependence of body condition, growth, and habitat temperature in chub mackerel (Scomber japonicus)

The density dependence of growth and body condition have important impacts on fish population dynamics and fisheries management. Although population density is known to affect the temperature of the habitat selected, how this affects the density dependence of growth and body condition remains unclear. Here, we investigated annual changes in body condition, habitat temperature, and cohort-specific growth of chub mackerel (Scomber japonicus) in the western North Pacific and examined quarterly changes in the density dependence of body condition. We hypothesized that chub mackerel body condition is affected both directly (e.g., through competition for food) and indirectly (through changes in habitat temperature) by the abundance of both conspecifics (i.e., chub mackerel) and heterospecifics (the Japanese sardine Sardinops melanostictus). Indeed, chub mackerel body condition, habitat temperature, and growth all decreased with increasing conspecific and heterospecific abundance. Mean annual growth rates in chub mackerel were positively corelated with body condition. The best model showed that conspecific and/or heterospecific abundance had strong negative effects on chub mackerel body condition in all seasons, and influenced habitat temperature in some seasons. By contrast, temperature effects on body condition were weak. Therefore, direct effects likely have more impact than indirect effects on density-dependent body condition and growth.

ecology↗

bioRxiv2020

Length-length and length-weight relationships for four small pelagic fishes in the Kuroshio-Oyashio current system

Length-length relationships and length-weight relationships were estimated for four small pelagic fishes (Japanese sardine Sardinops melanostictus, Japanese anchovy Engraulis japonicus, chub mackerel Scomber japonicus, and spotted mackerel Scomber australasicus) in the Kuroshio-Oyashio current system. Fish samples were collected from surface-midwater trawl surveys and commercial purse-seine fisheries between September and October of 2020 in the western North Pacific. Total length (TL), fork length (FL), and standard length (SL) were measured to 0.01 cm, and whole body weight (W) was measured to the nearest 0.01 g for each individual. All length-length relationships (TL-FL, TL-SL, and FL-SL) were highly significant (p < 0.0001), with r2 > 0.98 in all species. Length-weight relationships (W-TL, W-FL, and W-SL) were also highly significant (p < 0.0001), with r2> 0.98 in all species. This study provides a useful reference for biological studies and stock assessments of these small pelagic fishes.

ecology↗

bioRxiv2020

Spatio-temporal spawning patterns and early growth of Japanese sardine in the western North Pacific during the recent stock increase

Spatio-temporal patterns in spawning influence growth and survival by affecting the environment experienced by offspring during their early life stages. Therefore, identifying changes in spawning patterns can help researchers understand population dynamics and recruitment fluctuations. The Japanese sardine Sardinops melanostictus is a small pelagic fish that undergoes large stock fluctuations. Although spawning patterns are known to change spatially and temporally with stock abundance, little information is available on the processes underlying stock increases. This study aimed to describe changes in spawning pattern and early growth of Japanese sardine during the recent period of stock increase, and to clarify the effects of different spawning periods on offspring growth. We examined trends in egg abundance in the western North Pacific in 2004-2018 and analyzed hatch dates and growth trajectories by otolith microstructure analysis of juveniles from the Kuroshio-Oyashio transitional region (the species main nursery area). During the study period, the main spawning area shifted from the western to the eastern part of this region off Japan, and spawning in the eastern part roughly coincided with juvenile hatch dates. Hatch dates also shifted from mid-March at the earliest to February and early March from 2013 onwards. Although early-hatched cohorts (which originate offshore of eastern Japan) experienced slower initial growth, they likely played an important role in the recent stock increase. Successful recruitment of these cohorts may have been facilitated by factors such as early hatching and transport to the nursery, which reduces the frequency of predator encounters.

ecology↗

bioRxiv2020

Solving the sex ratio scandal in Melittobia wasps

The scandalous sex ratio behaviour of Melittobia wasps has long posed one of the greatest problems for the field of sex allocation. In contrast to the predictions of theory, and the behaviour of numerous other organisms, laboratory experiments have found that Melittobia females do not produce less female-biased offspring sex ratios when more females lay eggs on a patch. We resolve this scandal, by showing that, in nature, females of M. australica have sophisticated sex ratio behaviour, where their strategy also depends upon whether they have dispersed from the patch where they emerged. When females have not dispersed, they will be laying eggs with close relatives, which keeps local mate competition high, even with multiple females, and so they are selected to produce consistently female-biased sex ratios. Laboratory experiments mimic these conditions. In contrast, when females disperse, they will be interacting with non-relatives, and so they adjust their sex ratio depending upon the number of females laying eggs. Consequently, females appear to use dispersal status as an indirect cue of relatedness, and whether they should adjust their sex ratio in response to the number of females laying eggs on the patch.

evolutionary biology↗

bioRxiv2020

Evolution of nuptial gifts and its coevolutionary dynamics with "masculine" female traits for multiple mating

Many male animals donate nutritive materials during courtship or mating to their female mates. Donation of large-sized gifts, though costly to prepare, can result in increased sperm transfer during mating and delayed remating of the females, resulting in a higher paternity Nuptial gifting sometimes causes severe female-female competition for obtaining gifts (i.e., sex-role reversal in mate competition) and female polyandry, changing the intensity of sperm competition and the resultant paternity gains. We built a theoretical model to analyze such coevolutionary feedbacks between nuptial gift size (male trait) and propensity for multiple mating (female trait). Our genetically explicit, individual-based computer simulations demonstrate that a positive correlation between donated gift size and the resultant paternity gain is a requisite for the co-occurrence of large-sized gifts and females competitive multiple mating for the gifts. When donation of gifts imposes monandry, exaggeration in nuptial gift size also occurs under the assumption that the last male monopolizes paternity. We also analyzed the causes and consequences of the evolution of a female persistence trait in trading of nuptial gifts, that is, double receptacles for nuptial gifts known to occur in an insect group with a "female penis" (Neotrogla spp.).

evolutionary biology↗